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Xiaoping Chen
Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China

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Journal article
Published: 10 August 2021 in LWT
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Peanut sprouts (PSs) are edible food with a high nutritional value. It is well known that different light treatments during seedling germination affect the nutritional elements of PSs. However, the comprehensive exploration of the chemical profile variation after light and dark treatments is not widely used in PSs due to the lack of high-throughout examination technology. In the present study, a widely targeted method based on UHPLC-QTRAP-MS/MS equipment was carried out to identify and screen differential metabolites. A total of 797 metabolites were identified from PSs, and 97 differential metabolites were screened between light and dark treatment groups. The majority of phytochemical compounds, such as flavonoids, alkaloids, nucleotides, amino acids, saccharides, and alcohols, were significantly up-regulated in PSs germinated under the dark conditions, which were positively related to the large-scale metabolic data of human diseases by KEGG metabolic pathway analysis. Collectively, our data suggest that the seeds should be protected from exposure to light during PS germination, which might improve the nutritional value of the final peanut product.

ACS Style

Yuan Xiao; Hao Liu; Haifen Li; Qinjian Liu; Qing Lu; Rajeev K. Varshney; Xiaoping Chen; Yanbin Hong. Widely targeted metabolomics characterizes the dynamic changes of chemical profile in postharvest peanut sprouts grown under the dark and light conditions. LWT 2021, 152, 112283 .

AMA Style

Yuan Xiao, Hao Liu, Haifen Li, Qinjian Liu, Qing Lu, Rajeev K. Varshney, Xiaoping Chen, Yanbin Hong. Widely targeted metabolomics characterizes the dynamic changes of chemical profile in postharvest peanut sprouts grown under the dark and light conditions. LWT. 2021; 152 ():112283.

Chicago/Turabian Style

Yuan Xiao; Hao Liu; Haifen Li; Qinjian Liu; Qing Lu; Rajeev K. Varshney; Xiaoping Chen; Yanbin Hong. 2021. "Widely targeted metabolomics characterizes the dynamic changes of chemical profile in postharvest peanut sprouts grown under the dark and light conditions." LWT 152, no. : 112283.

Research article
Published: 26 June 2021 in Plant Biotechnology Journal
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Single cell RNA-seq (scRNA-seq) has been highlighted as a powerful tool for the description of the human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single-cells were divided into eight cell-clusters based on reported marker genes by applying scRNA-seq. Further, a pseudo-time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re-investigation of the primordium-driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA-seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA-seq values. Additionally, peanut AHL23 (AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA-seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea. We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.

ACS Style

Hao Liu; Dongxiu Hu; Puxuan Du; Liping Wang; Xuanqiang Liang; Haifen Li; Qing Lu; Shaoxiong Li; Haiyan Liu; Xiaoping Chen; Rajeev K Varshney; Yanbin Hong. Single‐cell RNA‐seq Describes the Transcriptome Landscape and Identifies Critical Transcription Factors in the Leaf Blade of the Allotetraploid Peanut ( Arachis hypogaea L .). Plant Biotechnology Journal 2021, 1 .

AMA Style

Hao Liu, Dongxiu Hu, Puxuan Du, Liping Wang, Xuanqiang Liang, Haifen Li, Qing Lu, Shaoxiong Li, Haiyan Liu, Xiaoping Chen, Rajeev K Varshney, Yanbin Hong. Single‐cell RNA‐seq Describes the Transcriptome Landscape and Identifies Critical Transcription Factors in the Leaf Blade of the Allotetraploid Peanut ( Arachis hypogaea L .). Plant Biotechnology Journal. 2021; ():1.

Chicago/Turabian Style

Hao Liu; Dongxiu Hu; Puxuan Du; Liping Wang; Xuanqiang Liang; Haifen Li; Qing Lu; Shaoxiong Li; Haiyan Liu; Xiaoping Chen; Rajeev K Varshney; Yanbin Hong. 2021. "Single‐cell RNA‐seq Describes the Transcriptome Landscape and Identifies Critical Transcription Factors in the Leaf Blade of the Allotetraploid Peanut ( Arachis hypogaea L .)." Plant Biotechnology Journal , no. : 1.

Journal article
Published: 26 April 2021 in International Journal of Molecular Sciences
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Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut.

ACS Style

Sunil Gangurde; Spurthi Nayak; Pushpesh Joshi; Shilp Purohit; Hari Sudini; Annapurna Chitikineni; Yanbin Hong; Baozhu Guo; Xiaoping Chen; Manish Pandey; Rajeev Varshney. Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut. International Journal of Molecular Sciences 2021, 22, 4491 .

AMA Style

Sunil Gangurde, Spurthi Nayak, Pushpesh Joshi, Shilp Purohit, Hari Sudini, Annapurna Chitikineni, Yanbin Hong, Baozhu Guo, Xiaoping Chen, Manish Pandey, Rajeev Varshney. Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut. International Journal of Molecular Sciences. 2021; 22 (9):4491.

Chicago/Turabian Style

Sunil Gangurde; Spurthi Nayak; Pushpesh Joshi; Shilp Purohit; Hari Sudini; Annapurna Chitikineni; Yanbin Hong; Baozhu Guo; Xiaoping Chen; Manish Pandey; Rajeev Varshney. 2021. "Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut." International Journal of Molecular Sciences 22, no. 9: 4491.

Article
Published: 10 April 2021 in Agronomy Journal
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The morphological and molecular diversity of 101 peanut varieties from South China were analyzed to identify distinctness among these varieties. No significant difference was observed for 6 morphological characteristics whereas a range of 0.25‐0.51 of diversity index was observed for 11 morphological characteristics, with an average value of 0.39. Molecular characterization with 40 highly polymorphic SSRs generated a total of 167 alleles ranging from 2‐6 alleles per marker with average 4.18 alleles per marker. The polymorphism information content (PIC) of these markers varied from 0.79 to 0.26 with an average value of 0.55 per marker. The diversity analysis using morphological and genotyping data grouped all the varieties into 7 and 6 clusters, respectively, and varieties released by the same province tended to be grouped in same cluster. Mantel testing revealed that the correlations between the similarity coefficient matrixes of the morphological characteristics and SSR markers of different varieties were weak (r = 0.347), implying that deployment of more SSR markers is needed for achieving distinctness among these peanut varieties. Nevertheless, the combination of morphological characteristics and SSR markers will effectively increase the accuracy of distinctiveness identification. This article is protected by copyright. All rights reserved

ACS Style

Yanbin Hong; Manish K. Pandey; Qing Lu; Hao Liu; Sunil S. Gangurde; Shaoxiong Li; Haiyan Liu; Haifen Li; Xuanqiang Liang; Rajeev K. Varshney; Xiaoping Chen. Genetic diversity and distinctness based on morphological and SSR markers in peanut. Agronomy Journal 2021, 1 .

AMA Style

Yanbin Hong, Manish K. Pandey, Qing Lu, Hao Liu, Sunil S. Gangurde, Shaoxiong Li, Haiyan Liu, Haifen Li, Xuanqiang Liang, Rajeev K. Varshney, Xiaoping Chen. Genetic diversity and distinctness based on morphological and SSR markers in peanut. Agronomy Journal. 2021; ():1.

Chicago/Turabian Style

Yanbin Hong; Manish K. Pandey; Qing Lu; Hao Liu; Sunil S. Gangurde; Shaoxiong Li; Haiyan Liu; Haifen Li; Xuanqiang Liang; Rajeev K. Varshney; Xiaoping Chen. 2021. "Genetic diversity and distinctness based on morphological and SSR markers in peanut." Agronomy Journal , no. : 1.

Journal article
Published: 16 December 2020 in Journal of Fungi
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Aflatoxin-affected groundnut or peanut presents a major global health issue to both commercial and subsistence farming. Therefore, understanding the genetic and molecular mechanisms associated with resistance to aflatoxin production during host–pathogen interactions is crucial for breeding groundnut cultivars with minimal level of aflatoxin contamination. Here, we performed gene expression profiling to better understand the mechanisms involved in reduction and prevention of aflatoxin contamination resulting from Aspergillus flavus infection in groundnut seeds. RNA sequencing (RNA-Seq) of 16 samples from different time points during infection (24 h, 48 h, 72 h and the 7th day after inoculation) in U 4-7-5 (resistant) and JL 24 (susceptible) genotypes yielded 840.5 million raw reads with an average of 52.5 million reads per sample. A total of 1779 unique differentially expressed genes (DEGs) were identified. Furthermore, comprehensive analysis revealed several pathways, such as disease resistance, hormone biosynthetic signaling, flavonoid biosynthesis, reactive oxygen species (ROS) detoxifying, cell wall metabolism and catabolizing and seed germination. We also detected several highly upregulated transcription factors, such as ARF, DBB, MYB, NAC and C2H2 in the resistant genotype in comparison to the susceptible genotype after inoculation. Moreover, RNA-Seq analysis suggested the occurrence of coordinated control of key pathways controlling cellular physiology and metabolism upon A. flavus infection, resulting in reduced aflatoxin production.

ACS Style

Pooja Soni; Spurthi N. Nayak; Rakesh Kumar; Manish K. Pandey; Namita Singh; Hari K. Sudini; Prasad Bajaj; Jake C. Fountain; Prashant Singam; Yanbin Hong; Xiaoping Chen; Weijian Zhuang; Boshou Liao; Baozhu Guo; Rajeev K. Varshney. Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut. Journal of Fungi 2020, 6, 370 .

AMA Style

Pooja Soni, Spurthi N. Nayak, Rakesh Kumar, Manish K. Pandey, Namita Singh, Hari K. Sudini, Prasad Bajaj, Jake C. Fountain, Prashant Singam, Yanbin Hong, Xiaoping Chen, Weijian Zhuang, Boshou Liao, Baozhu Guo, Rajeev K. Varshney. Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut. Journal of Fungi. 2020; 6 (4):370.

Chicago/Turabian Style

Pooja Soni; Spurthi N. Nayak; Rakesh Kumar; Manish K. Pandey; Namita Singh; Hari K. Sudini; Prasad Bajaj; Jake C. Fountain; Prashant Singam; Yanbin Hong; Xiaoping Chen; Weijian Zhuang; Boshou Liao; Baozhu Guo; Rajeev K. Varshney. 2020. "Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut." Journal of Fungi 6, no. 4: 370.

Journal article
Published: 03 August 2020 in Scientific Reports
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Peanut pods develop underground, which is the most salient characteristic in peanut. However, its developmental transcriptome remains largely unknown. In the present study, we sequenced over one billion transcripts to explore the developmental transcriptome of peanut pod using Illumina sequencing. Moreover, we identified and quantified the abundances of 165,689 transcripts in seed and shell tissues along with a pod developmental gradient. The dynamic changes of differentially expressed transcripts (DETs) were described in seed and shell. Additionally, we found that photosynthetic genes were not only pronouncedly enriched in aerial pod, but also played roles in developing pod under dark condition. Genes functioning in photomorphogenesis showed distinct expression profiles along subterranean pod development. Clustering analysis unraveled a dynamic transcriptome, in which transcripts for DNA synthesis and cell division during pod expansion were transitioning to transcripts for cell expansion and storage activity during seed filling. Collectively, our study formed a transcriptional baseline for peanut fruit development under dark condition.

ACS Style

Hao Liu; Xuanqiang Liang; Qing Lu; Haifen Li; Haiyan Liu; Shaoxiong Li; Rajeev Varshney; Yanbin Hong; Xiaoping Chen. Global transcriptome analysis of subterranean pod and seed in peanut (Arachis hypogaea L.) unravels the complexity of fruit development under dark condition. Scientific Reports 2020, 10, 1 -12.

AMA Style

Hao Liu, Xuanqiang Liang, Qing Lu, Haifen Li, Haiyan Liu, Shaoxiong Li, Rajeev Varshney, Yanbin Hong, Xiaoping Chen. Global transcriptome analysis of subterranean pod and seed in peanut (Arachis hypogaea L.) unravels the complexity of fruit development under dark condition. Scientific Reports. 2020; 10 (1):1-12.

Chicago/Turabian Style

Hao Liu; Xuanqiang Liang; Qing Lu; Haifen Li; Haiyan Liu; Shaoxiong Li; Rajeev Varshney; Yanbin Hong; Xiaoping Chen. 2020. "Global transcriptome analysis of subterranean pod and seed in peanut (Arachis hypogaea L.) unravels the complexity of fruit development under dark condition." Scientific Reports 10, no. 1: 1-12.

Journal article
Published: 01 November 2019 in BMC Genomics
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Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Results A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. Conclusions The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.

ACS Style

Qing Lu; Yanbin Hong; Shaoxiong Li; Hao Liu; Haifen Li; Jianan Zhang; Haofa Lan; Haiyan Liu; Xingyu Li; Shijie Wen; GuiYuan Zhou; Rajeev K. Varshney; Huifang Jiang; Xiaoping Chen; Xuanqiang Liang. Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.). BMC Genomics 2019, 20, 799 -9.

AMA Style

Qing Lu, Yanbin Hong, Shaoxiong Li, Hao Liu, Haifen Li, Jianan Zhang, Haofa Lan, Haiyan Liu, Xingyu Li, Shijie Wen, GuiYuan Zhou, Rajeev K. Varshney, Huifang Jiang, Xiaoping Chen, Xuanqiang Liang. Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.). BMC Genomics. 2019; 20 (1):799-9.

Chicago/Turabian Style

Qing Lu; Yanbin Hong; Shaoxiong Li; Hao Liu; Haifen Li; Jianan Zhang; Haofa Lan; Haiyan Liu; Xingyu Li; Shijie Wen; GuiYuan Zhou; Rajeev K. Varshney; Huifang Jiang; Xiaoping Chen; Xuanqiang Liang. 2019. "Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)." BMC Genomics 20, no. 1: 799-9.

Journal article
Published: 01 July 2019 in Molecular Plant
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Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

ACS Style

Xiaoping Chen; Qing Lu; Hao Liu; Jianan Zhang; Yanbin Hong; Haofa Lan; Haifen Li; Jinpeng Wang; Haiyan Liu; Shaoxiong Li; Manish K. Pandey; Zhikang Zhang; GuiYuan Zhou; Jigao Yu; Guoqiang Zhang; Jiaqing Yuan; Xingyu Li; Shijie Wen; Fanbo Meng; Shanlin Yu; Xiyin Wang; Kadambot Siddique; Zhong-Jian Liu; Andrew H. Paterson; Rajeev K. Varshney; Xuanqiang Liang. Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement. Molecular Plant 2019, 12, 920 -934.

AMA Style

Xiaoping Chen, Qing Lu, Hao Liu, Jianan Zhang, Yanbin Hong, Haofa Lan, Haifen Li, Jinpeng Wang, Haiyan Liu, Shaoxiong Li, Manish K. Pandey, Zhikang Zhang, GuiYuan Zhou, Jigao Yu, Guoqiang Zhang, Jiaqing Yuan, Xingyu Li, Shijie Wen, Fanbo Meng, Shanlin Yu, Xiyin Wang, Kadambot Siddique, Zhong-Jian Liu, Andrew H. Paterson, Rajeev K. Varshney, Xuanqiang Liang. Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement. Molecular Plant. 2019; 12 (7):920-934.

Chicago/Turabian Style

Xiaoping Chen; Qing Lu; Hao Liu; Jianan Zhang; Yanbin Hong; Haofa Lan; Haifen Li; Jinpeng Wang; Haiyan Liu; Shaoxiong Li; Manish K. Pandey; Zhikang Zhang; GuiYuan Zhou; Jigao Yu; Guoqiang Zhang; Jiaqing Yuan; Xingyu Li; Shijie Wen; Fanbo Meng; Shanlin Yu; Xiyin Wang; Kadambot Siddique; Zhong-Jian Liu; Andrew H. Paterson; Rajeev K. Varshney; Xuanqiang Liang. 2019. "Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement." Molecular Plant 12, no. 7: 920-934.

Journal article
Published: 25 June 2019 in International Journal of Molecular Sciences
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Peanuts with high oleic acid content are usually considered to be beneficial for human health and edible oil storage. In breeding practice, peanut lines with high monounsaturated fatty acids are selected using fatty acid desaturase 2 (FAD2), which is responsible for the conversion of oleic acid (C18:1) to linoleic acid (C18:2). Here, comparative transcriptomics were used to analyze the global gene expression profile of high- and normal-oleic peanut cultivars at six time points during seed development. First, the mutant type of FAD2 was determined in the high-oleic peanut (H176). The result suggested that early translation termination occurred simultaneously in the coding sequence of FAD2-A and FAD2-B, and the cultivar H176 is capable of utilizing a potential germplasm resource for future high-oleic peanut breeding. Furthermore, transcriptomic analysis identified 74 differentially expressed genes (DEGs) involved in lipid metabolism in high-oleic peanut seed, of which five DEGs encoded the fatty acid desaturase. Aradu.XM2MR belonged to the homologous gene of stearoyl-ACP (acyl carrier protein) desaturase 2 (SAD2) that converted the C18:0 into C18:1. Further subcellular localization studies indicated that FAD2 was located at the endoplasmic reticulum (ER), and Aradu.XM2MR was targeted to the plastid in Arabidopsis protoplast cells. To examine the dynamic mechanism of this finding, we focused on the peroxidase (POD)-mediated fatty acid (FA) degradation pathway. The fad2 mutant significantly increased the POD activity and H2O2 concentration at the early stage of seed development, implying that redox signaling likely acted as a messenger to connect the signaling transduction between the high-oleic content and Aradu.XM2MR transcription level. Taken together, transcriptome analysis revealed the feedback mechanism of SAD2 (Aradu.XM2MR) associated with FAD2 mutation during the seed developmental stage, which could provide a potential peanut breeding strategy based on identified candidate genes to improve the content of oleic acid.

ACS Style

Hao Liu; Jianzhong Gu; Qing Lu; Haifen Li; Yanbin Hong; Xiaoping Chen; Li Ren; Li Deng; Xuanqiang Liang. Transcriptomic Analysis Reveals the High-Oleic Acid Feedback Regulating the Homologous Gene Expression of Stearoyl-ACP Desaturase 2 (SAD2) in Peanuts. International Journal of Molecular Sciences 2019, 20, 3091 .

AMA Style

Hao Liu, Jianzhong Gu, Qing Lu, Haifen Li, Yanbin Hong, Xiaoping Chen, Li Ren, Li Deng, Xuanqiang Liang. Transcriptomic Analysis Reveals the High-Oleic Acid Feedback Regulating the Homologous Gene Expression of Stearoyl-ACP Desaturase 2 (SAD2) in Peanuts. International Journal of Molecular Sciences. 2019; 20 (12):3091.

Chicago/Turabian Style

Hao Liu; Jianzhong Gu; Qing Lu; Haifen Li; Yanbin Hong; Xiaoping Chen; Li Ren; Li Deng; Xuanqiang Liang. 2019. "Transcriptomic Analysis Reveals the High-Oleic Acid Feedback Regulating the Homologous Gene Expression of Stearoyl-ACP Desaturase 2 (SAD2) in Peanuts." International Journal of Molecular Sciences 20, no. 12: 3091.

Review
Published: 03 June 2019 in Toxins
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Aflatoxin is considered a “hidden poison” due to its slow and adverse effect on various biological pathways in humans, particularly among children, in whom it leads to delayed development, stunted growth, liver damage, and liver cancer. Unfortunately, the unpredictable behavior of the fungus as well as climatic conditions pose serious challenges in precise phenotyping, genetic prediction and genetic improvement, leaving the complete onus of preventing aflatoxin contamination in crops on post-harvest management. Equipping popular crop varieties with genetic resistance to aflatoxin is key to effective lowering of infection in farmer’s fields. A combination of genetic resistance for in vitro seed colonization (IVSC), pre-harvest aflatoxin contamination (PAC) and aflatoxin production together with pre- and post-harvest management may provide a sustainable solution to aflatoxin contamination. In this context, modern “omics” approaches, including next-generation genomics technologies, can provide improved and decisive information and genetic solutions. Preventing contamination will not only drastically boost the consumption and trade of the crops and products across nations/regions, but more importantly, stave off deleterious health problems among consumers across the globe.

ACS Style

Manish K. Pandey; Rakesh Kumar; Arun K. Pandey; Pooja Soni; Sunil S. Gangurde; Hari K. Sudini; Jake C. Fountain; Boshou Liao; Haile Desmae; Patrick Okori; Xiaoping Chen; Huifang Jiang; Venugopal Mendu; Hamidou Falalou; Samuel Njoroge; James Mwololo; Baozhu Guo; Weijian Zhuang; Xingjun Wang; Xuanqiang Liang; Rajeev K. Varshney. Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices. Toxins 2019, 11, 315 .

AMA Style

Manish K. Pandey, Rakesh Kumar, Arun K. Pandey, Pooja Soni, Sunil S. Gangurde, Hari K. Sudini, Jake C. Fountain, Boshou Liao, Haile Desmae, Patrick Okori, Xiaoping Chen, Huifang Jiang, Venugopal Mendu, Hamidou Falalou, Samuel Njoroge, James Mwololo, Baozhu Guo, Weijian Zhuang, Xingjun Wang, Xuanqiang Liang, Rajeev K. Varshney. Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices. Toxins. 2019; 11 (6):315.

Chicago/Turabian Style

Manish K. Pandey; Rakesh Kumar; Arun K. Pandey; Pooja Soni; Sunil S. Gangurde; Hari K. Sudini; Jake C. Fountain; Boshou Liao; Haile Desmae; Patrick Okori; Xiaoping Chen; Huifang Jiang; Venugopal Mendu; Hamidou Falalou; Samuel Njoroge; James Mwololo; Baozhu Guo; Weijian Zhuang; Xingjun Wang; Xuanqiang Liang; Rajeev K. Varshney. 2019. "Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices." Toxins 11, no. 6: 315.

Journal article
Published: 07 December 2018 in BMC Genomics
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Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. However, only a limited number of QTLs have been used in marker-assisted selection (MAS) because of unfavorable epistatic interactions between QTLs in different genetic backgrounds. Thus, it is essential to identify consensus QTLs across different environments and genetic backgrounds for use in MAS. Here, we used QTL meta-analysis to identify a set of consensus QTLs for yield and disease resistance related traits in peanut. A new integrated consensus genetic map with 5874 loci was constructed. The map comprised 20 linkage groups (LGs) and was up to a total length of 2918.62 cM with average marker density of 2.01 loci per centimorgan (cM). A total of 292 initial QTLs were projected on the new consensus map, and 40 meta-QTLs (MQTLs) for yield and disease resistance related traits were detected on four LGs. The genetic intervals of these consensus MQTLs varied from 0.20 cM to 7.4 cM, which is narrower than the genetic intervals of the initial QTLs, meaning they may be suitable for use in MAS. Importantly, a region of the map that previously co-localized multiple major QTLs for pod traits was narrowed from 3.7 cM to 0.7 cM using an overlap region of four MQTLs for yield related traits on LG A05, which corresponds to a physical region of about 630.3 kb on the A05 pseudomolecule of peanut, including 38 annotated candidate genes (54 transcripts) related to catalytic activity and metabolic process. Additionally, one major MQTL for late leaf spot (LLS) was identified in a region of about 0.38 cM. BLAST searches identified 26 candidate genes (30 different transcripts) in this region, some of which were annotated as related to regulation of disease resistance in different plant species. Combined with the high-density marker consensus map, all the detected MQTLs could be useful in MAS. The biological functions of the 64 candidate genes should be validated to unravel the molecular mechanisms of yield and disease resistance in peanut.

ACS Style

Qing Lu; Hao Liu; Yanbin Hong; Haifen Li; Haiyan Liu; Xingyu Li; Shijie Wen; GuiYuan Zhou; Shaoxiong Li; Xiaoping Chen; Xuanqiang Liang. Consensus map integration and QTL meta-analysis narrowed a locus for yield traits to 0.7 cM and refined a region for late leaf spot resistance traits to 0.38 cM on linkage group A05 in peanut (Arachis hypogaea L.). BMC Genomics 2018, 19, 1 -10.

AMA Style

Qing Lu, Hao Liu, Yanbin Hong, Haifen Li, Haiyan Liu, Xingyu Li, Shijie Wen, GuiYuan Zhou, Shaoxiong Li, Xiaoping Chen, Xuanqiang Liang. Consensus map integration and QTL meta-analysis narrowed a locus for yield traits to 0.7 cM and refined a region for late leaf spot resistance traits to 0.38 cM on linkage group A05 in peanut (Arachis hypogaea L.). BMC Genomics. 2018; 19 (1):1-10.

Chicago/Turabian Style

Qing Lu; Hao Liu; Yanbin Hong; Haifen Li; Haiyan Liu; Xingyu Li; Shijie Wen; GuiYuan Zhou; Shaoxiong Li; Xiaoping Chen; Xuanqiang Liang. 2018. "Consensus map integration and QTL meta-analysis narrowed a locus for yield traits to 0.7 cM and refined a region for late leaf spot resistance traits to 0.38 cM on linkage group A05 in peanut (Arachis hypogaea L.)." BMC Genomics 19, no. 1: 1-10.

Correction
Published: 31 July 2018 in Frontiers in Plant Science
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Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)

ACS Style

Qing Lu; Haifen Li; Yanbin Hong; Guoqiang Zhang; Shijie Wen; Xingyu Li; GuiYuan Zhou; Shaoxiong Li; Hao Liu; Haiyan Liu; Zhongjian Liu; Rajeev K. Varshney; Xiaoping Chen; Xuanqiang Liang. Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). Frontiers in Plant Science 2018, 9, 1099 .

AMA Style

Qing Lu, Haifen Li, Yanbin Hong, Guoqiang Zhang, Shijie Wen, Xingyu Li, GuiYuan Zhou, Shaoxiong Li, Hao Liu, Haiyan Liu, Zhongjian Liu, Rajeev K. Varshney, Xiaoping Chen, Xuanqiang Liang. Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). Frontiers in Plant Science. 2018; 9 ():1099.

Chicago/Turabian Style

Qing Lu; Haifen Li; Yanbin Hong; Guoqiang Zhang; Shijie Wen; Xingyu Li; GuiYuan Zhou; Shaoxiong Li; Hao Liu; Haiyan Liu; Zhongjian Liu; Rajeev K. Varshney; Xiaoping Chen; Xuanqiang Liang. 2018. "Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)." Frontiers in Plant Science 9, no. : 1099.

Original research article
Published: 03 May 2018 in Frontiers in Plant Science
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Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that A. ipaensis experienced a whole-genome duplication event after the divergence of Glycine max. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from A. ipaensis and A. duranensis, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new FAD2 homologous genes were identified from A. ipaensis and one was completely homologous at the amino acid level with FAD2 from A. hypogaea. The availability of the A. ipaensis and A. duranensis genomic assemblies will advance our knowledge of the peanut genome.

ACS Style

Qing Lu; Haifen Li; Yanbin Hong; Guoqiang Zhang; Shijie Wen; Xingyu Li; GuiYuan Zhou; Shaoxiong Li; Hao Liu; Haiyan Liu; Zhongjian Liu; Rajeev Varshney; Xiaoping Chen; Xuanqiang Liang. Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). Frontiers in Plant Science 2018, 9, 604 .

AMA Style

Qing Lu, Haifen Li, Yanbin Hong, Guoqiang Zhang, Shijie Wen, Xingyu Li, GuiYuan Zhou, Shaoxiong Li, Hao Liu, Haiyan Liu, Zhongjian Liu, Rajeev Varshney, Xiaoping Chen, Xuanqiang Liang. Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). Frontiers in Plant Science. 2018; 9 ():604.

Chicago/Turabian Style

Qing Lu; Haifen Li; Yanbin Hong; Guoqiang Zhang; Shijie Wen; Xingyu Li; GuiYuan Zhou; Shaoxiong Li; Hao Liu; Haiyan Liu; Zhongjian Liu; Rajeev Varshney; Xiaoping Chen; Xuanqiang Liang. 2018. "Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)." Frontiers in Plant Science 9, no. : 604.

Comparative study
Published: 18 April 2018 in International Journal of Molecular Sciences
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Peanuts (Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the high content of OA in peanut oil is beneficial for human health and long-term storage due to its antioxidant activity. However, the dynamic changes in proteomics related to OA accumulation during seed development still remain largely unexplored. In the present study, a comparative proteome analysis based on iTRAQ (isobaric Tags for Relative and Absolute Quantification) was performed to identify the critical candidate factors involved in OA formation. A total of 389 differentially expressed proteins (DEPs) were identified between high-oleate cultivar Kainong176 and low-oleate cultivar Kainong70. Among these DEPs, 201 and 188 proteins were upregulated and downregulated, respectively. In addition, these DEPs were categorized into biosynthesis pathways of unsaturated FAs at the early stage during the high-oleic peanut seed development, and several DEPs involved in lipid oxidation pathway were found at the stage of seed maturation. Meanwhile, 28 DEPs were sporadically distributed in distinct stages of seed formation, and their molecular functions were directly correlated to FA biosynthesis and degradation. Fortunately, the expression of FAB2 (stearoyl-acyl carrier protein desaturase), the rate-limiting enzyme in the upstream biosynthesis process of OA, was significantly increased in the early stage and then decreased in the late stage of seed development in the high-oleate cultivar Kainong176. Furthermore, real-time PCR verified the expression pattern of FAB2 at the mRNA level, which was consistent with its protein abundance. However, opposite results were found for the low-oleate cultivar Kainong70. Overall, the comparative proteome analysis provided valuable insight into the molecular dynamics of OA accumulation during peanut seed development.

ACS Style

Hao Liu; Haifen Li; Jianzhong Gu; Li Deng; Li Ren; Yanbin Hong; Qing Lu; Xiaoping Chen; Xuanqiang Liang. Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis. International Journal of Molecular Sciences 2018, 19, 1235 .

AMA Style

Hao Liu, Haifen Li, Jianzhong Gu, Li Deng, Li Ren, Yanbin Hong, Qing Lu, Xiaoping Chen, Xuanqiang Liang. Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis. International Journal of Molecular Sciences. 2018; 19 (4):1235.

Chicago/Turabian Style

Hao Liu; Haifen Li; Jianzhong Gu; Li Deng; Li Ren; Yanbin Hong; Qing Lu; Xiaoping Chen; Xuanqiang Liang. 2018. "Identification of the Candidate Proteins Related to Oleic Acid Accumulation during Peanut (Arachis hypogaea L.) Seed Development through Comparative Proteome Analysis." International Journal of Molecular Sciences 19, no. 4: 1235.